COMP305. Part II.
Genetic Algorithms.
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Topic 1.
Biological motivation for
Genetic Algorithms.
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Darwinian theory of Evolution (macroscopic).
Species adapt to the environment via
natural selection.
The selection favors those species for survival
and further evolution that are best adapted to the
environmental condition –
“survival of the fittest”.
Phenotype is the manner of response and
physical embodiment of an individual. There
occur small, apparently random and undirected
variations between the phenotypes of parents and
their offspring.
These mutations prevail through selection, if
they prove their worth in light of the current
environment; otherwise they perish.
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Darwinian theory of Evolution (macroscopic).
Production of offspring is the basic driving force for selection.
In a favorable environment population grows exponentially.
This growth is generally limited by finite resources.
When resources are no longer sufficient to support all
individuals in a population,
only the fittest, i.e. those most effectively exploiting the
resources, survive and produce offspring.
In a hostile environment organisms in a population are at a
selective advantage to exploit resources most effectively.
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NeoDarwinism synthetic theory of
Evolution
(microscopic).
All living organisms consist of cells.
Each cell in an organism contains the
same set of one or more chromosomes –
Chromosomes are strings of DNA that
serve as a blueprint for the organism.
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Nature 171, 737-738 (1953) © Macmillan
Publishers Ltd.
Molecular structure of Nucleic Acids
WATSON, J. D. & CRICK, F. H. C.
Medical Research Council Unit for the
Study of Molecular Structure of Biological
Systems, Cavendish Laboratory, Cambridge.
Figure 1
This figure is purely
diagrammatic. The two
ribbons symbolize the two
phosphate-sugar chains,
and the horizontal rods the
pairs of bases holding the
chains together. The
vertical line marks the fibre
axis.
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Born: London, England, July 25, 1920
Died: London, England, April 16, 1958
Pioneer Molecular Biologist
responsible for much of the research and
discovery work that led to the understanding
of the structure of DNA
It was in Randall's lab that she crossed paths with Maurice Wilkins.
She and Wilkins led separate research groups and had separate projects,
although both were concerned with DNA. When Randall gave Franklin
responsibility for her DNA project, no one had worked on it for months.
Wilkins was away at the time, and when he returned he misunderstood her role,
behaving as though she were a technical assistant. Both scientists were actually
peers. His mistake, acknowledged but never overcome, was not surprising given the
climate for women at the university then. Only males were allowed in the university
dining rooms, and after hours Franklin's colleagues went to men-only pubs. At one
point, Wilkins showed Watson one of Franklin's crystallographic portraits of DNA.
When he saw the picture, the solution became apparent to him, and the results went
into an article in Nature almost immediately. Franklin's work did appear as a
supporting article in the same issue of the journal.
A debate about the amount of credit due to Franklin continues. What is clear is that
she did have a meaningful role in learning the structure of DNA and that she was a
scientist of the first rank.
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NeoDarwinism synthetic theory of
Evolution
(microscopic).
A chromosome can be conceptually divided into genes --Gene is a functional block of DNA coding a particular protein.
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NeoDarwinism - synthetic theory of Evolution
(microscopic). DNA code.
DNA alphabet:
A - adenine,
G - guanine,
T - thymine,
C – cytosine.
DNA molecule consists of
 two ribbons of phosphate-sugar chains, and
 the horizontal rods the pairs of nitrogenous
bases holding the chains together
There exist only four different nitrogenous bases
in DNA: adenine, guanine, thymine, cytosine.
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NeoDarwinism - synthetic theory of Evolution
(microscopic). DNA code.
DNA alphabet:
A - adenine,
G - guanine,
T - thymine,
C - cytosine.
 The two chains held together by hydrogen bonds formed between pairs of bases.
 Pairing is highly specific. It is always that
Adenine pairs with Thymine, A = T; and Guanine pairs with Cytosine, G = C.
The precise sequence of bases carries the genetic information.
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NeoDarwinism - synthetic theory of Evolution
(microscopic). DNA code.
DNA alphabet:
A - adenine,
G - guanine,
T - thymine,
C - cytosine.
 The precise sequence of bases carries the genetic information.
Gene is a functional block of DNA coding a particular protein.
Problem: there are just 4 letters in the DNA alphabet to code
20 amino acids found in proteins
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NeoDarwinism - synthetic theory of Evolution
(microscopic). DNA code.
DNA alphabet:
A - adenine,
G - guanine,
T - thymine,
C - cytosine.
 Gene is a functional block of DNA coding a particular protein.
Problem: there are just 4 letters in the DNA alphabet to code
20 amino acids found in proteins
Solution: 1. there can not be one to one,
i.e. one DNA letter per one amino acid, match.
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NeoDarwinism - synthetic theory of Evolution
(microscopic). DNA code.
DNA alphabet:
A - adenine,
G - guanine,
T - thymine,
C - cytosine.
Problem: 4 letters in the DNA alphabet to code 20 amino acids found in proteins
Solution: 1. there can not be one to one match.
2. There can not be a two nucleic bases to one amino acid match either,
as it gives just 42 =16 different pairs of nucleotides < 20 .
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NeoDarwinism - synthetic theory of Evolution
(microscopic). DNA code.
DNA alphabet:
A - adenine,
G - guanine,
T - thymine,
C - cytosine.
Problem: 4 letters in the DNA alphabet to code 20 amino acids found in proteins
Solution: 3 nucleic bases in combination as a triplet are required to code
for each amino acid, as this gives 43 = 64 possible combinations or codons
=> the genetic code is based on the triplet codons.
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NeoDarwinism - synthetic theory of Evolution
(microscopic). DNA code.
T
T
Problem: 4 letters in the DNA alphabet
to code 20 amino acids found in proteins
Solution: the genetic code is based on the
triplet codons.
The genetic code.
 The genetic code is universal, as the codons that code for amino acids are
the same in bacteria, plants and animals .
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NeoDarwinism - synthetic theory of Evolution
(microscopic). DNA code.
T
T
Problem: 4 letters in the DNA alphabet
to code 20 amino acids found in proteins
Solution: the genetic code is based on the
triplet codons.
The genetic code.
 The genetic code is universal, as the codons that code for amino acids are
the same in bacteria, plants and animals .
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DNA code. Crossing-over (Recombination).
Organisms with unpaired sets of chromosomes are called haploid.
Organisms, whose chromosomes are arranged in pairs are called
diploid. Most sexually reproducing organisms are diploid.
During sexual reproduction,
crossing-over or recombination of genes in parental chromosomes occurs.
In each parent cell, a pair of chromosomes first doubles,
then the chromosomes exchange genes, and
finally produce four gametes, single chromosomes, ready to
couple with the other parent gametes to form a new diploid cell
Formation
of gametes
(Meiosis).
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DNA code. Mutations.
T
T
Mutation
is a random change of
“letter”, single nucleotide in a
chromosome.
The genetic code.
 Mutations usually result from copying errors in parental
chromosomes and then are reproduced in offspring.
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NeoDarwinism synthetic theory of
Evolution
(microscopic).
Gene is a functional block of DNA coding a particular protein,
see “gene encodes a trait, e.g. eye colour”.
Different possible settings for a trait, e.g. blue, brown, hazel eye colour,
are called alleles.
Each gene is located at a particular locus (position) on the chromosome.
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Gene is a functional block
of DNA coding a particular
protein, see “gene encodes a
trait, e.g. eye colour”.
NeoDarwinism synthetic theory of
Evolution
(microscopic).
The complete collection of all genetic material,
all chromosomes taken together,
is called the organisms genome or genotype.
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NeoDarwinism - synthetic theory of Evolution
(microscopic).
Genes are transfer units of heredity. Genes are occasionally
changed by mutations.
Phenotype expresses complex interaction within the genotype as
well as its interaction with environment.
Modern biochemistry
and genetics explain
microscopic
mechanisms of
heredity.
Source: Howell, F. C. (1966) Early man (pp. 41-45). Time-Life International.
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NeoDarwinism - synthetic theory of Evolution
(microscopic).
Genes are transfer units of heredity, and genotype is the total
genetic information of an individual.
Selection acts on an individual, thus
an individual is a selection unit.
Population is the evolving unit. Population as a unit confines a
common gene pool including genotypes of all individuals.
Modern biochemistry
and genetics explain
microscopic
mechanisms of
heredity.
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Natural Evolution. What is the Fitness ?
Individual fitness is measured indirectly
as the individual growth rate in
comparison to others.
The fitness is the individual
propensity to survive and reproduce in
a particular environment.
Thus, Natural Selection according to the
individual fitness
is NOT an active driving force,
IS differential survival and
reproduction within a population.
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Natural Evolution. What is the Fitness ?
Individual fitness is measured indirectly
as the individual growth rate in
comparison to others.
The fitness is the individual
propensity to survive and reproduce in SO, what is the fitness?
a particular environment.
Can we
Thus, Natural Selection according to the 1. map a given genotype into the
corresponding phenotype and
individual fitness
2. map the phenotype into the
is NOT an active driving force,
individual fitness to survive and
IS differential survival and
reproduce ?
reproduction within a population.
Not, actually…
But the idea is so beautiful...
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